The biggest problem faced with the USB Flash Drive is the security of data and the protection from infected viruses mad malware that corrupt the machines that are connected to it or when comes to data sharing.
The solution for this is now available with features like password protection, encryption, anti-virus. Now your flash drive can perform scans on the foreign system even if it does not have its own virus protection. This will help to ensure that your flash drive does not get infected. Even though you take this precaution, I would also advise scanning the flash drive as soon as you plug it back into your regular PC. This will help catch anything that your portable virus scanner did not catch.
As of passwords, it can also be helpful to have a password manager software on your USB Flash drive. When you are on your home PC, Internet Explorer will help you manage many of your passwords to websites. But if you have a password manager, it makes it easy to keep track of your passwords. Of course, the password database itself is encrypted, and you can keep the encrypted database within the encrypted virtual drive, yet another feature supporting the USB Flash drive.
What some people do is to save some seconds, they just take away the USB without properly doing the 'safely remove device' procedure. This sometimes results in loss of data as the data gets corrupt and is lost in this procedure. It is highly recommended that not to try such things if your data is really important.
As for security, these also act as as one of the largest threat to any organization, as these are so handy that the important and secured data can easily be taken away without any labor and the company can face higher consequences than imagined. So it is prohibited in many corporates that carry a USB Flash device.
The best secure USB flash drives feature Advanced Encryption Standard (AES) symmetric encryption. This is one of the newest government- and corporate-grade encryption standards, and its complexity is more than sufficient to protect your data. It's popularity is just being spreading as the requirement of security is increasing both in normal users and corporate users. A small add-on cost will be worth every penny as it will definitely help in the long run.Different manufactures offer different key lengths or implementations.
Choose a USB flash drive with proper encryption complexity that's comfortable for you.
When deploying these devices, make sure you update the company's security policy to address their use in the organization. In addition, you may want to maintain a password database for the devices for you can remember all the passwords of different USB's. Otherwise, if you forget their passwords, the cost of data recovery might sometimes not be equal to the corporate value of the data.